Two-color Real-time/End-point Quantitation of MicroRNAs (miRNAs)

ABSTRACT

The present invention is directed to methods, reagents, kits, and compositions for detecting target polynucleotide sequences, especially small target polynucleotides such as miRNAs, between two samples. A pair of linker probes can be employed in two different reactions to query a particular species of target polynucleotide. A pair of detector probes, a single forward primer specific for the target polynucleotide, and a reverse primer can be employed in an amplification reaction to query the difference in expression level of the target polynucleotide between the two samples. In some embodiments a plurality of small miRNAs are queried with a plurality of linker probes. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of application Ser. No. 11/232,475,filed on Sep. 21, 2005, which is incorporated herein by reference.

This application claims a priority benefit under 35 U.S.C. §119(e) fromU.S. Patent Application No. 60/612,199, filed on Sep. 21, 2005, which isincorporated herein by reference.

FIELD

The present teachings are in the field of molecular and cell biology,specifically in the field of detecting target polynucleotides such asmiRNA.

INTRODUCTION

RNA interference (RNAi) is a highly coordinated, sequence-specificmechanism involved in posttranscriptional gene regulation. During theinitial steps of process, a ribonuclease (RNase) II-like enzyme calledDicer reduces long double-strand RNA (dsRNA) and complex hairpinprecursors into: 1) small interfering RNAs (siRNA) that degrademessenger RNA (mRNA) and 2) micro RNAs (miRNAs) that can target mRNAsfor cleavage or attenuate translation.

The siRNA class of molecules is thought to be comprised of 21-23nucleotide (nt) depluxes with characteristic dinucleotide 3′ overhangs(Ambros et al., 2003, RNA, 9 (3), 277-279). siRNA has been shown to actas the functional intermediate in RNAi, specifically directing cleavageof complementary mRNA targets in a process that is commonly regarded tobe an antiviral cellular defense mechanism (Elbashir et al., 2001,Nature, 411:6836), 494-498, Elbashir et al., 2001, Genes andDevelopment, 15 (2), 188-200). Target RNA cleavage is catalyzed by theRNA-induced silencing complex (RISC), which functions as a siRNAdirected endonuclease (reviewed in Bartel, 2004, Cell, 116 (2),281-297).

Micro RNAs (miRNAs) typically comprise single-stranded, endogenousoligoribonucleotides of roughly 22 (18-25) bases in length that areprocessed from larger stem-looped precursor RNAs. The first genesrecognized to encode miRNAs, lin-4 and let-7 of C. elegans, wereidentified on the basis of the developmental timing defects associatedwith the loss-of-function mutations (Lee et al., 1993, Cell, 75 (5),843-854; Reinhart et al., 2000, Nature, 403, (6772), 901-906; reviewedby Pasquinelli et al., 2002, Annual Review of Cell and DevelopmentalBiology, 18, 495-513). The breadth and importance of miRNA-directed generegulation are coming into focus as more miRNAs and regulatory targetsand functions are discovered. To date, a total of at least 700 miRNAshave been identified in C. elegans, Drosophila (Fire et al., 1998,Nature, 391 (6669(, 805-811), mouse, human (Lagos-Quintana et al., 2001,Science, 294 (5543), 853-858), and plants (Reinhart et al., 2002, Genesand Development, 16 (13), 1616-1626). Their sequences are typicallyconserved among different species. Size ranges from 18 to 25 nucleotidesfor miRNAs are the most commonly observed to date.

The function of most miRNAs is not known. Recently discovered miRNAfunctions include control of cell proliferation, cell death, and fatmetabolism in flies (Brennecke et al., 2003, cell, 113 (1), 25-36; Xu etal, 2003, Current Biology, 13 (9), 790-795), neuronal patterning innematodes (Johnston and Hobert, 2003, Nature, 426 (6968), 845-849),modulation of hematopoietic lineage differentiation in mammals (Chen etal., 2004, Science, 303 (5654), 83-87), and control of leaf and flowerdevelopment in plants (Aukerman and Sakai, 2003, Plant Cell, 15 (11),2730-2741; Chen, 2003, Science, 303 (5666):2022-2025; Emery et al.,2003, Current Biology, 13 (20), 1768-1774; Palatnik et al., 2003,Nature, 425 (6955), 257-263). There is speculation that miRNAs mayrepresent a new aspect of gene regulation.

Most miRNAs have been discovered by cloning. While there are a fewcloning kits available for researchers from Ambion and QIAGEN, theprocess is laborious and not very accurate. Further, there has beenlittle reliable technology available for miRNA quantitation (Allawi etal., Third Wave Technologies, RNA. 2004 July; 10(7):1153-61). Northernblotting has been used but results are not quantitative (Lagos-Quitanaet al., 2001, Science, 294 (5543), 853-854). Many miRNA researchers areinterested in monitoring the level of the miRNAs at different tissues,at the different stages of development, or after treatment with variouschemical agents. However, the short length of miRNAs has made theirstudy difficult.

SUMMARY

The present teachings provide a method for quantifying a small targetpolynucleotide in each of two samples comprising; providing a firstreaction mixture comprising a small target polynucleotide from a firstsample, and a first linker probe, wherein the first linker probecomprises a 3′ target-specific portion a, a stem, and a loop, whereinthe 3′ target-specific portion base pairs with the 3′ end of the targetpolynucleotide; providing a second reaction mixture comprising a smalltarget polynucleotide from a second sample, and a second linker probe,wherein the second linker probe comprises a 3′ target-specific portion,a stem, and a loop, wherein the 3′ target-specific portion base pairswith the 3′ end of the target polynucleotide, wherein the small targetpolynucleotide in the first reaction mixture is the same species as thesmall target polynucleotide in the second reaction mixture; hybridizingthe first linker probe to the small target polynucleotide in the firstreaction mixture to form a first target-linker probe complex andhybridizing the second linker probe to the small target polynucleotidein the second reaction mixture to form a second target-linker probecomplex; combining the first target-linker probe complex and the secondtarget-linker probe complex to form a pooled reaction mixture, whereinthe pooled reaction mixture comprises a first extension reaction productand a second extension reaction product; amplifying the first extensionreaction product and the second extension reaction product in thepresence of a first detector probe and a second detector probe to forman amplified first extension reaction product and an amplified secondextension reaction product, wherein the first detector probe correspondsto the amplified first extension reaction product and the seconddetector probe corresponds to the second amplified second extensionreaction product; and, detecting the quantity of the small targetpolynucleotide in the two samples by comparing the first detector probeand the second detector probe.

In some embodiments, the present teachings provide a kit comprising; areaction vessel comprising a first linker probe; a reaction vesselcomprising a second linker probe; wherein the first linker probe and thesecond linker probe comprise the same 3′ target specific portion anddifferent sample identifying portions.

In some embodiments, the present teachings provide a reaction mixturecomprising; a first linker probe hybridized to a first species of asmall target polynucleotide, and a second linker probe hybridized to asecond species of the small target polynucleotide, wherein the firstlinker probe comprises a first sample identifying portion and the secondlinker probe comprises a second sample identifying portion.

BRIEF DESCRIPTION OF THE DRAWINGS

The skilled artisan will understand that the drawings, described below,are for illustration purposes only. The drawings are not intended tolimit the scope of the present teachings in any way.

FIG. 1 depicts an overview according to some embodiments of the presentteachings.

FIG. 2 depicts certain aspects of various compositions as used invarious methods according to some embodiments of the present teachings.

FIG. 3 depicts certain methods according to some embodiments of thepresent teachings.

DESCRIPTION OF EXEMPLARY EMBODIMENTS

Aspects of the present teachings may be further understood in light ofthe following examples, which should not be construed as limiting thescope of the present teachings in any way. The section headings usedherein are for organizational purposes only and are not to be construedas limiting the described subject matter in any way. All literature andsimilar materials cited in this application, including but not limitedto, patents, patent applications, articles, books, treatises, andinternet web pages are expressly incorporated by reference in theirentirety for any purpose. When definitions of terms in incorporatedreferences appear to differ from the definitions provided in the presentteachings, the definition provided in the present teachings shallcontrol. It will be appreciated that there is an implied “about” priorto the temperatures, concentrations, times, etc discussed in the presentteachings, such that slight and insubstantial deviations are within thescope of the present teachings herein. In this application, the use ofthe singular includes the plural unless specifically stated otherwise.For example, “a linker probe” means that more than one linker probe canbe present; for example but without limitation, one or more copies of aparticular linker probe species, as well as one or more versions of aparticular linker probe type, for example but not limited to, amultiplicity of different first linker probes querying a multiplicity ofdifferent target polynucleotide species in a first sample. Also, the useof “comprise”, “comprises”, “comprising”, “contain”, “contains”,“containing”, “include”, “includes”, and “including” are not intended tobe limiting. It is to be understood that both the foregoing generaldescription and the following detailed description are exemplary andexplanatory only and are not restrictive of the invention.

SOME DEFINITIONS

As used herein, the term “target polynucleotide” refers to apolynucleotide sequence that is sought to be detected. The targetpolynucleotide can be obtained from any source, and can comprise anynumber of different compositional components. For example, the targetcan be nucleic acid (e.g. DNA or RNA), transfer RNA, siRNA, and any of avariety of small non-coding RNAs (see for example Science, 309:1567-1569(2005)), and can comprise nucleic acid analogs or other nucleic acidmimics. The target can be methylated, non-methylated, or both. Thetarget can be bisulfite-treated and non-methylated cytosines convertedto uracil. Further, it will be appreciated that “target polynucleotide”can refer to the target polynucleotide itself, as well as surrogatesthereof, for example amplification products, and native sequences. Insome embodiments, the target polynucleotide is a miRNA molecule. In someembodiments, the target polynucleotide is a small target polynucleotide.In some embodiments, the small target polynucleotide can be 25 or fewernucleotides in length. In some embodiments, the small targetpolynucleotide can be 23 or fewer nucleotide bases in length. In someembodiments, the target polynucleotide lacks a poly-A tail. In someembodiments, the target polynucleotide is a small DNA molecule derivedfrom a degraded source, such as can be found in for example but notlimited to forensics samples (see for example Butler, 2001, Forensic DNATyping: Biology and Technology Behind STR Markers. The targetpolynucleotides of the present teachings can be derived from any of anumber of sources, including without limitation, viruses, prokaryotes,eukaryotes, for example but not limited to plants, fungi, and animals.These sources may include, but are not limited to, whole blood, a tissuebiopsy, lymph, bone marrow, amniotic fluid, hair, skin, semen,biowarfare agents, anal secretions, vaginal secretions, perspiration,saliva, buccal swabs, various environmental samples (for example,agricultural, water, and soil), research samples generally, purifiedsamples generally, cultured cells, and lysed cells. It will beappreciated that target polynucleotides can be isolated from samplesusing any of a variety of procedures known in the art, for example theApplied Biosystems ABI Prism™ 6100 Nucleic Acid PrepStation, and the ABIPrism™ 6700 Automated Nucleic Acid Workstation, Boom et al., U.S. Pat.No. 5,234,809, mirVana RNA isolation kit (Ambion), etc, as well asapproaches described in U.S. Provisional Application Pure miRNA SamplePreparation Method, filed Sep. 12, 2005 to Lao. It will be appreciatedthat target polynucleotides can be cut or sheared prior to analysis,including the use of such procedures as mechanical force, sonication,restriction endonuclease cleavage, or any method known in the art. Ingeneral, the target polynucleotides of the present teachings will besingle stranded, though in some embodiments the target polynucleotidecan be double stranded, and a single strand can result fromdenaturation.

As used herein, the term “3′ end region of the target polynucleotide”refers to the region of the target to which the 3′ target specificportion of the linker probe hybridizes. In some embodiments there can bea gap between the 3′ end region of the target polynucleotide and the 5′end of the linker probe, with extension reactions filling in the gap,though generally such scenarios are not preferred because of the likelydestabilizing effects on the duplex. In some embodiments, a miRNAmolecule is the target, in which case the term “3′ end region of themiRNA” is used.

As used herein, the term “linker probe” refers to a molecule comprisinga 3′ target specific portion, a stem, and a loop, that can be extendedfrom its 3′ end when hybridized to a corresponding targetpolynucleotide. Illustrative linker probes are depicted in FIG. 2A, andelsewhere in the present teachings. It will be appreciated that thelinker probes, as well as the PCR primers of the present teachings, canbe comprised of ribonucleotides, deoxynucleotides, modifiedribonucleotides, modified deoxyribonucleotides, modifiedphosphate-sugar-backbone oligonucleotides, nucleotide analogs, orcombinations thereof. For some illustrative teachings of variousnucleotide analogs etc, see Fasman, 1989, Practical Handbook ofBiochemistry and Molecular Biology, pp. 385-394, CRC Press, Boca Raton,Fla., Loakes, N.A.R. 2001, vol 29:2437-2447, and Pellestor et al., Int JMal Med. 2004 April; 13(4):521-5.), references cited therein, and recentarticles citing these reviews. It will be appreciated that the selectionof the linker probes to query a given target polynucleotide sequence,and the selection of which collection of target polynucleotide sequencesto query in a given reaction with which collection of linker probes,will involve procedures generally known in the art, and can involve theuse of algorithms to select for those sequences with minimal secondaryand tertiary structure, those targets with minimal sequence redundancywith other regions of the genome, those target regions with desirablethermodynamic characteristics, and other parameters desirable for thecontext at hand.

As used herein, the term “3′ target-specific portion” refers to thesingle stranded portion of a linker probe that is complementary to atarget polynucleotide. The 3′ target-specific portion is locateddownstream from the stem of the linker probe. Generally, the 3′target-specific portion is between 6 and 8 nucleotides long. In someembodiments, the 3′ target-specific portion is 7 nucleotides long. Itwill be appreciated that routine experimentation can produce otherlengths, and that 3′ target-specific portions that are longer than 8nucleotides or shorter than 6 nucleotides are also contemplated by thepresent teachings. Generally, the 3′-most nucleotides of the 3′target-specific portion should have minimal complementarity overlap, orno overlap at all, with the 3′ nucleotides of the forward primer; itwill be appreciated that overlap in these regions can produce undesiredprimer dimer amplification products in subsequent amplificationreactions. In some embodiments, the overlap between the 3′-mostnucleotides of the 3′ target-specific portion and the 3′ nucleotides ofthe forward primer is 0, 1, 2, or 3 nucleotides. In some embodiments,greater than 3 nucleotides can be complementary between the 3′-mostnucleotides of the 3′ target-specific portion and the 3′ nucleotides ofthe forward primer, but generally such scenarios will be accompanied byadditional non-complementary nucleotides interspersed therein. In someembodiments, modified bases such as LNA can be used in the 3′ targetspecific portion to increase the Tm of the linker probe (see for examplePetersen et al., Trends in Biochemistry (2003), 21:2:74-81). In someembodiments, universal bases can be used, for example to allow forsmaller libraries of linker probes. Universal bases can also be used inthe 3′ target specific portion to allow for the detection of unknowntargets. For some descriptions of universal bases, see for exampleLoakes et al., Nucleic Acids Research, 2001, Volume 29, No. 12,2437-2447. In some embodiments, modifications including but not limitedto LNAs and universal bases can improve reverse transcriptionspecificity and potentially enhance detection specificity.

As used herein, the term “stem” refers to the double stranded region ofthe linker probe that is between the 3′ target-specific portion and theloop. Generally, the stem is between 6 and 20 nucleotides long (that is,6-20 complementary pairs of nucleotides, for a total of 12-40 distinctnucleotides). In some embodiments, the stem is 8-14 nucleotides long.Those in the art will appreciate that stems shorter that 6 nucleotidesand longer than 20 nucleotides can be identified in the course ofroutine methodology and without undue experimentation, and that suchshorter and longer stems are contemplated by the present teachings. Insome embodiments, the stem can comprise an identifying portion such as azipcode.

As used herein, the term “loop” refers to a region of the linker probethat is located between the two complementary strands of the stem, asdepicted in FIG. 2A and elsewhere in the present teachings. Typically,the loop comprises single stranded nucleotides, though other moietiesmodified DNA or RNA, Carbon spacers such as C18, and/or PEG(polyethylene glycol) are also possible. Generally, the loop is between4 and 20 nucleotides long. In some embodiments, the loop is between 14and 18 nucleotides long. In some embodiments, the loop is 16 nucleotideslong. Those in the art will appreciate that loops shorter that 4nucleotides and longer than 20 nucleotides can be identified in thecourse of routine methodology and without undue experimentation, andthat such shorter and longer loops are contemplated by the presentteachings. In some embodiments, the loop can comprise a reverse PCRprimer portion.

As used herein, the term “identifying portion” refers to a moiety ormoieties that can be used to identify a particular linker probe species,and as a result determine the sample of origin of a targetpolynucleotide sequence, and can refer to a variety of distinguishablemoieties including zipcodes, a known number of nucleobases, andcombinations thereof. In some embodiments, an identifying portion, or anidentifying portion complement, can hybridize to a detector probe,thereby allowing detection of a target polynucleotide sequence in adecoding reaction. The terms “identifying portion complement” typicallyrefers to at least one oligonucleotide that comprises at least onesequence of nucleobases that are at least substantially complementary toand hybridize with their corresponding identifying portion. Typically,identifying portions and their corresponding identifying portioncomplements are selected to minimize: internal, self-hybridization;cross-hybridization with different identifying portion species,nucleotide sequences in a reaction composition, including but notlimited to gDNA, different species of identifying portion complements,or target-specific portions of probes, and the like; but should beamenable to facile hybridization between the identifying portion and itscorresponding identifying portion complement. Identifying portionsequences and identifying portion complement sequences can be selectedby any suitable method, for example but not limited to, computeralgorithms such as described in PCT Publication Nos. WO 96/12014 and WO96/41011 and in European Publication No. EP 799,897; and the algorithmand parameters of SantaLucia (Proc. Natl. Acad. Sci. 95:1460-65 (1998)).Descriptions of identifying portions can be found in, among otherplaces, U.S. Pat. Nos. 6,309,829 (referred to as “tag segment” therein);6,451,525 (referred to as “tag segment” therein); 6,309,829 (referred toas “tag segment” therein); 5,981,176 (referred to as “gridoligonucleotides” therein); 5,935,793 (referred to as “identifier tags”therein); and PCT Publication No. WO 01/92579 (referred to as“addressable support-specific sequences” therein). In some embodiments,the stem of the linker probe, the loop of the linker probe, orcombinations thereof can comprise an identifying portion, and thedetector probe can hybridize to the corresponding identifying portion.In some embodiments, the detector probe can hybridize to both theidentifying portion as well as sequence corresponding to the targetpolynucleotide. In some embodiments, at least two identifying portion:identifying portion complement duplexes have melting temperatures thatfall within a Δ T_(m) range (T_(max)-T_(min)) of no more than 10° C. ofeach other. In some embodiments, at least two identifying portion:identifying portion complement duplexes have melting temperatures thatfall within at T_(m) range of 5° C. or less of each other. In someembodiments, at least two identifying portion: identifying portioncomplement duplexes have melting temperatures that fall within a Δ T_(m)range of 2° C. or less of each other.

As used herein, the term “extension reaction” refers to an elongationreaction in which the 3′ target specific portion of a linker probe isextended to form an extension reaction product comprising a strandcomplementary to the target polynucleotide. In some embodiments, thetarget polynucleotide is a miRNA molecule and the extension reaction isa reverse transcription reaction comprising a reverse transcriptase. Insome embodiments, the extension reaction is a reverse transcriptionreaction comprising a polymerase derived from a Eubacteria. In someembodiments, the extension reaction can comprise rTth polymerase, forexample as commercially available from Applied Biosystems catalog numberN808-0192, and N808-0098. In some embodiments, the target polynucleotideis a miRNA or other RNA molecule, and as such it will be appreciatedthat the use of polymerases that also comprise reverse transcriptionproperties can allow for some embodiments of the present teachings tocomprise a first reverse transcription reaction followed thereafter byan amplification reaction, thereby allowing for the consolidation of tworeactions in essentially a single reaction. In some embodiments, thetarget polynucleotide is a small DNA molecule and the extension reactioncomprises a polymerase and results in the synthesis of a 2^(nd) strandof DNA. In some embodiments, the consolidation of the extension reactionand a subsequent amplification reaction is further contemplated by thepresent teachings.

As used herein, the term “primer portion” refers to a region of apolynucleotide sequence that can serve directly, or by virtue of itscomplement, as the template upon which a primer can anneal for any of avariety of primer nucleotide extension reactions known in the art (forexample, PCR). It will be appreciated by those of skill in the art thatwhen two primer portions are present on a single polynucleotide, theorientation of the two primer portions is generally different. Forexample, one PCR primer can directly hybridize to a first primerportion, while the other PCR primer can hybridize to the complement ofthe second primer portion. In addition, “universal” primers and primerportions as used herein are generally chosen to be as unique as possiblegiven the particular assays and host genomes to ensure specificity ofthe assay.

As used herein, the term “forward primer” refers to a primer thatcomprises an extension reaction product portion and a tail portion. Theextension reaction product portion of the forward primer hybridizes tothe extension reaction product. Generally, the extension reactionproduct portion of the forward primer is between 9 and 19 nucleotides inlength. In some embodiments, the extension reaction product portion ofthe forward primer is 16 nucleotides. The tail portion is locatedupstream from the extension reaction product portion, and is notcomplementary with the extension reaction product; after a round ofamplification however, the tail portion can hybridize to complementarysequence of amplification products. Generally, the tail portion of theforward primer is between 5-8 nucleotides long. In some embodiments, thetail portion of the forward primer is 6 nucleotides long. Those in theart will appreciate that forward primer tail portion lengths shorterthan 5 nucleotides and longer than 8 nucleotides can be identified inthe course of routine methodology and without undue experimentation, andthat such shorter and longer forward primer tail portion lengths arecontemplated by the present teachings. Further, those in the art willappreciate that lengths of the extension reaction product portion of theforward primer shorter than 9 nucleotides in length and longer than 19nucleotides in length can be identified in the course of routinemethodology and without undue experimentation, and that such shorter andlonger extension reaction product portion of forward primers arecontemplated by the present teachings.

As used herein, the term “reverse primer” refers to a primer that whenextended forms a strand complementary to the target polynucleotide. Insome embodiments, the reverse primer corresponds with a region of theloop of the linker probe. Following the extension reaction, the forwardprimer can be extended to form a second strand product. The reverseprimer hybridizes with this second strand product, and can be extendedto continue the amplification reaction. In some embodiments, the reverseprimer corresponds with a region of the loop of the linker probe, aregion of the stem of the linker probe, a region of the targetpolynucleotide, or combinations thereof. Generally, the reverse primeris between 13-16 nucleotides long. In some embodiments the reverseprimer is 14 nucleotides long. In some embodiments, the reverse primercan further comprise a non-complementary tail region, though such a tailis not required. In some embodiments, the reverse primer is a “universalreverse primer,” which indicates that the sequence of the reverse primercan be used in a plurality of different reactions querying differenttarget polynucleotides, but that the reverse primer nonetheless is thesame sequence.

The term “upstream” as used herein takes on, its customary meaning inmolecular biology, and refers to the location of a region of apolynucleotide that is on the 5′ side of a “downstream” region.Correspondingly, the term “downstream” refers to the location of aregion of a polynucleotide that is on the 3′ side of an “upstream”region.

As used herein, the term “hybridization” refers to the complementarybase-pairing interaction of one nucleic acid with another nucleic acidthat results in formation of a duplex, triplex, or other higher-orderedstructure, and is used herein interchangeably with “annealing.”Typically, the primary interaction is base specific, e.g., NT and G/C,by Watson/Crick and Hoogsteen-type hydrogen bonding. Base-stacking andhydrophobic interactions can also contribute to duplex stability.Conditions for hybridizing detector probes and primers to complementaryand substantially complementary target sequences are well known, e.g.,as described in Nucleic Acid Hybridization, A Practical Approach, B.Hames and S. Higgins, eds., IRL Press, Washington, D.C. (1985) and J.Wetmur and N. Davidson, Mol. Biol. 31:349 et seq. (1968). In general,whether such annealing takes place is influenced by, among other things,the length of the polynucleotides and the complementary, the pH, thetemperature, the presence of mono- and divalent cations, the proportionof G and C nucleotides in the hybridizing region, the viscosity of themedium, and the presence of denaturants. Such variables influence thetime required for hybridization. Thus, the preferred annealingconditions will depend upon the particular application. Such conditions,however, can be routinely determined by the person of ordinary skill inthe art without undue experimentation. It will be appreciated thatcomplementarity need not be perfect; there can be a small number of basepair mismatches that will minimally interfere with hybridization betweenthe target sequence and the single stranded nucleic acids of the presentteachings. However, if the number of base pair mismatches is so greatthat no hybridization can occur under minimally stringent conditionsthen the sequence is generally not a complementary target sequence.Thus, complementarity herein is meant that the probes or primers aresufficiently complementary to the target sequence to hybridize under theselected reaction conditions to achieve the ends of the presentteachings.

As used herein, the term “amplifying” refers to any means by which atleast a part of a target polynucleotide, target polynucleotidesurrogate, or combinations thereof, is reproduced, typically in atemplate-dependent manner, including without limitation, a broad rangeof techniques for amplifying nucleic acid sequences, either linearly orexponentially. Exemplary procedures for performing an amplifying stepinclude the polymerase chain reaction (PCR). Descriptions of additionaltechniques that can be used in the present teachings can be found in,among other places, Sambrook et al. Molecular Cloning, 3^(rd) Edition,;Ausbel et al.; PCR Primer: A Laboratory Manual, Diffenbach, Ed., ColdSpring Harbor Press (1995); The Electronic Protocol Book, ChangBioscience (2002), Msuih et al., J. Clin. Micro. 34:501-07 (1996); TheNucleic Acid Protocols Handbook, R. Rapley, ed., Humana Press, Totowa,N.J. (2002); Abramson et al., Curr Opin Biotechnol. 1993 February;4(1):41-7, U.S. Pat. No. 6,027,998; U.S. Pat. No. 6,605,451, Barany etal., PCT Publication No. WO 97/31256; Wenz et al., PCT Publication No.WO 01/92579; Day et al., Genomics, 29(1): 152-162 (1995), Ehrlich etal., Science 252; 1643-50 (1991); Innis et al., PCR Protocols: A Guideto Methods and Applications, Academic Press (1990); Favis et al., NatureBiotechnology 18:561-64 (2000); and Rabenau et al., Infection 28:97-102(2000); Belgrader, Barany, and Lubin, Development of a MultiplexLigation Detection Reaction DNA Typing Assay, Sixth InternationalSymposium on Human Identification, 1995 (available on the world wide webat: promega.com/geneticidproc/ussymp6proc/blegrad.html); LCR KitInstruction Manual, Cat. #200520, Rev. #050002, Stratagene, 2002;Barany, Proc. Natl. Acad. Sci. USA 88:188-93 (1991); Bi and Sambrook,Nucl. Acids Res. 25:2924-2951 (1997); Zirvi et al., Nucl. Acid Res.27:e40i-viii (1999); Dean et al., Proc Natl Acad Sci USA 99:526.1-66(2002); Barany and Gelfand, Gene 109:1-11 (1991); Walker et al, Nucl.Acid Res. 20:1691-96 (1992); Polstra et al., BMC Inf. Dis. 2:18-(2002);Lage et al., Genome Res. 2003 February; 13(2):294-307, and Landegren etal., Science 241:1077-80 (1988), Demidov, V., Expert Rev Mol Diagn. 2002November; 2(6):542-8., Cook et al., J Microbiol Methods. 2003 May;53(2):165-74, Schweitzer et al., Curr Opin Biotechnol. 2001 February;12(1):21-7, U.S. Pat. No. 5,830,711, U.S. Pat. No. 6,027,889, U.S. Pat.No. 5,686,243, Published P.C.T. Application WO0056927A3, and PublishedP.C.T. Application WO9803673A1. In some embodiments, newly-formednucleic acid duplexes are not initially denatured, but are used in theirdouble-stranded form in one or more subsequent steps. An extensionreaction is an amplifying technique that comprises elongating a linkerprobe that is annealed to a template in the 5′ to 3′ direction using anamplifying means such as a polymerase and/or reverse transcriptase.According to some embodiments, with appropriate buffers, salts, pH,temperature, and nucleotide triphosphates, including analogs thereof,i.e., under appropriate conditions, a polymerase incorporatesnucleotides complementary to the template strand starting at the 3′-endof an annealed linker probe, to generate a complementary strand. In someembodiments, the polymerase used for extension lacks or substantiallylacks 5′ exonuclease activity. In some embodiments of the presentteachings, unconventional nucleotide bases can be introduced into theamplification reaction products and the products treated by enzymatic(e.g., glycosylases) and/or physical-chemical means in order to renderthe product incapable of acting as a template for subsequentamplifications. In some embodiments, uracil can be included as anucleobase in the reaction mixture, thereby allowing for subsequentreactions to decontaminate carryover of previous uracil-containingproducts by the use of uracil-N-glycosylase (see, for example PublishedP.C.T. Application WO9201814A2). In some embodiments of the presentteachings, any of a variety of techniques can be employed prior toamplification in order to facilitate amplification success, as describedfor example in Radstrom et al., Mol Biotechnol. 2004 February;26(2):133-46. In some embodiments, amplification can be achieved in aself-contained integrated approach comprising sample preparation anddetection, as described for example in U.S. Pat. Nos. 6,153,425 and6,649,378. Reversibly modified enzymes, for example but not limited tothose described in U.S. Pat. No. 5,773,258, are also within the scope ofthe disclosed teachings. The present teachings also contemplate variousuracil-based decontamination strategies, wherein for example uracil canbe incorporated into an amplification reaction, and subsequentcarry-over products removed with various glycosylase treatments (see forexample U.S. Pat. No. 5,536,649, and U.S. Provisional Application60/584,682 to Andersen et al.,). Those in the art will understand thatany protein with the desired enzymatic activity can be used in thedisclosed methods and kits. Descriptions of DNA polymerases, includingreverse transcriptases, uracil N-glycosylase, and the like, can be foundin, among other places, Twyman, Advanced Molecular Biology, BIOSScientific Publishers, 1999; Enzyme Resource Guide, rev. 092298,Promega, 1998; Sambrook and Russell; Sambrook et al.; Lehninger; PCR:The Basics; and Ausbel et al.

As used herein, the term “detector probe” refers to a molecule used inan amplification reaction, typically for quantitative or real-time PCRanalysis, as well as end-point analysis. Such detector probes can beused to monitor the amplification of the target polynucleotide. In someembodiments, detector probes present in an amplification reaction aresuitable for monitoring the amount of amplicon(s) produced as a functionof time. Such detector probes include, but are not limited to, the5′-exonuclease assay (TaqMan® probes described herein (see also U.S.Pat. No. 5,538,848) various stem-loop molecular beacons (see e.g., U.S.Pat. Nos. 6,103,476 and 5,925,517 and Tyagi and Kramer, 1996, NatureBiotechnology 14:303-308), stemless or linear beacons (see, e.g., WO99/21881), PNA Molecular Beacons™ (see, e.g., U.S. Pat. Nos. 6,355,421and 6,593,091), linear PNA beacons (see, e.g., Kubista et al., 2001,SPIE 4264:53-58), non-FRET probes (see, e.g., U.S. Pat. No. 6,150,097),Sunrise®/Amplifluor® probes (U.S. Pat. No. 6,548,250), stem-loop andduplex Scorpion™ probes (Solinas et al., 2001, Nucleic Acids Research29:E96 and U.S. Pat. No. 6,589,743), bulge loop probes (U.S. Pat. No.6,590,091), pseudo knot probes (U.S. Pat. No. 6,589,250), cyclicons(U.S. Pat. No. 6,383,752), MGB Eclipse™ probe (Epoch Biosciences),hairpin probes (U.S. Pat. No. 6,596,490), peptide nucleic acid (PNA)light-up probes, self-assembled nanoparticle probes, andferrocene-modified probes described, for example, in U.S. Pat. No.6,485,901; Mhlanga et al., 2001, Methods 25:463-471; Whitcombe et al.,1999, Nature Biotechnology. 17:804-807; Isacsson et al., 2000, MolecularCell Probes. 14:321-328; Svanvik et al., 2000, Anal Biochem. 281:26-35;Wolffs et al., 2001, Biotechniques 766:769-771; Tsourkas et al., 2002,Nucleic Acids Research. 30:4208-4215; Riccelli et al., 2002, NucleicAcids Research 30:4088-4093; Zhang et al., 2002 Shanghai. 34:329-332;Maxwell et al., 2002, J. Am. Chem. Soc. 124:9606-9612; Broude et al.,2002, Trends Biotechnol. 20:249-56; Huang et al., 2002, Chem Res.Toxicol. 15:118-126; and Yu et al., 2001, J. Am. Chem. Soc14:11155-11161. Detector probes can also comprise quenchers, includingwithout limitation black hole quenchers (Biosearch), Iowa Black (IDT),QSY quencher (Molecular Probes), and Dabsyl and Dabcelsulfonate/carboxylate Quenchers (Epoch). Detector probes can alsocomprise two probes, wherein for example a fluor is on one probe, and aquencher is on the other probe, wherein hybridization of the two probestogether on a target quenches the signal, or wherein hybridization onthe target alters the signal signature via a change in fluorescence.Detector probes can also comprise sulfonate derivatives of fluorescenindyes with SO3 instead of the carboxylate group, phosphoramidite forms offluorescein, phosphoramidite forms of CY 5 (commercially available forexample from Amersham). In some embodiments, interchelating labels areused such as ethidium bromide, SYBR® Green I (Molecular Probes), andPicoGreen® (Molecular Probes), thereby allowing visualization inreal-time, or end point, of an amplification product in the absence of adetector probe. In some embodiments, real-time visualization cancomprise both an intercalating detector probe and a sequence-baseddetector probe can be employed. In some embodiments, the detector probeis at least partially quenched when not hybridized to a complementarysequence in the amplification reaction, and is at least partiallyunquenched when hybridized to a complementary sequence in theamplification reaction. In some embodiments, the detector probes of thepresent teachings have a Tm of 63-69 C, though it will be appreciatedthat guided by the present teachings routine experimentation can resultin detector probes with other Tms. In some embodiments, probes canfurther comprise various modifications such as a minor groove binder(see for example U.S. Pat. No. 6,486,308) to further provide desirablethermodynamic characteristics. In some embodiments, detector probes cancorrespond to identifying portions or identifying portion complements.In some embodiments, the identifying portions or identifying portioncomplements, and the corresponding detector probes can vary by only twonucleotides. For example, a first identifying portion encoding a sampleA can differ from a second identifying portion encoding a sample B byonly two nucleotide bases. Correspondingly, the two detector probes candiffer from one another by only two nucleotide bases. Such aconfiguration can minimize unwanted variation between the activity ofthe two detector probes, thus improving the ability to accuratelyquantify the expression level difference between a given targetpolynucleotide between the two samples. In some embodiments, thedetector probes can differ from each other by as little as a singlenucleotide. In some embodiments, the detector probes can differ by threenucleotides. In some embodiments, the detector probes can differ by fournucleotides.

The term “corresponding” as used herein refers to a specificrelationship between the elements to which the term refers. Somenon-limiting examples of corresponding include: a linker probe cancorrespond with a target polynucleotide, and vice versa. A forwardprimer can correspond with a target polynucleotide, and vice versa. Alinker probe can correspond with a forward primer for a given targetpolynucleotide, and vice versa. The 3′ target-specific portion of thelinker probe can correspond with the 3′ region of a targetpolynucleotide, and vice versa. A detector probe can correspond with aparticular region of a target polynucleotide and vice versa. A detectorprobe can correspond with a particular identifying portion and viceversa. In some cases, the corresponding elements can be complementary.In some cases, the corresponding elements are not complementary to eachother, but one element can be complementary to the complement of anotherelement.

The term “or combinations thereof” as used herein refers to allpermutations and combinations of the listed items preceding the term.For example, “A, B, C, or combinations thereof” is intended to includeat least one of: A, B, C, AB, AC, BC, or ABC, and if order is importantin a particular context, also BA, CA, CB, CBA, BCA, ACB, BAC, or CAB.Continuing with this example, expressly included are combinations thatcontain repeats of one or more item or term, such as BB, AAA, AAB, BBC,AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan willunderstand that typically there is no limit on the number of items orterms in any combination, unless otherwise apparent from the context.

As used herein, the term “reaction vessel” generally refers to anycontainer in which a reaction can occur in accordance with the presentteachings. In some embodiments, a reaction vessel can be an eppendorftube, and other containers of the sort in common practice in modernmolecular biology laboratories. In some embodiments, a reaction vesselcan be a well in microtitre plate, a spot on a glass slide, or a well inan Applied Biosystems TaqMan Low Density Array for gene expression(formerly MicroCard™). For example, a plurality of reaction vessels canreside on the same support. In some embodiments, lab-on-a-chip likedevices, available for example from Caliper and Fluidgm, can provide forreaction vessels. In some embodiments, various microfluidic approachesas described in U.S. Provisional application Ser. No. 11/059,824 to Wenzet al., can be employed. It will be recognized that a variety ofreaction vessel are available in the art and within the scope of thepresent teachings.

As used herein, the term “detection” refers to any of a variety of waysof determining the presence and/or quantity and/or identity of a targetpolynucleotide. In some embodiments employing a donor moiety and signalmoiety, one may use certain energy-transfer fluorescent dyes. Certainnonlimiting exemplary pairs of donors (donor moieties) and acceptors(signal moieties) are illustrated, e.g., in U.S. Pat. Nos. 5,863,727;5,800,996; and 5,945,526. Use of some combinations of a donor and anacceptor have been called FRET (Fluorescent Resonance Energy Transfer).In some embodiments, fluorophores that can be used as signaling probesinclude, but are not limited to, rhodamine, cyanine 3 (Cy 3), cyanine 5(Cy 5), fluorescein, Vic™, Liz™, Tamra™, 5-Fam™, 6-Fam™, and Texas Red(Molecular Probes). (Vic™, Liz™ Tamra™, 5-Fam™, and 6-Fam™ (allavailable from Applied Biosystems, Foster City, Calif.). In someembodiments, the amount of detector probe that gives a fluorescentsignal in response to an excited light typically relates to the amountof nucleic acid produced in the amplification reaction. Thus, in someembodiments, the amount of fluorescent signal is related to the amountof product created in the amplification reaction. In such embodiments,one can therefore measure the amount of amplification product bymeasuring the intensity of the fluorescent signal from the fluorescentindicator. According to some embodiments, one can employ an internalstandard to quantify the amplification product indicated by thefluorescent signal. See, e.g., U.S. Pat. No. 5,736,333. Devices havebeen developed that can perform a thermal cycling reaction withcompositions containing a fluorescent indicator, emit a light beam of aspecified wavelength, read the intensity of the fluorescent dye, anddisplay the intensity of fluorescence after each cycle. Devicescomprising a thermal cycler, light beam emitter, and a fluorescentsignal detector, have been described, e.g., in U.S. Pat. Nos. 5,928,907;6,015,674; and 6,174,670, and include, but are not limited to the ABIPrism® 7700 Sequence Detection System (Applied Biosystems, Foster City,Calif.), the ABI GeneAmp® 5700 Sequence Detection System (AppliedBiosystems, Foster City, Calif.), the ABI GeneAmp® 7300 SequenceDetection System (Applied Biosystems, Foster City, Calif.), and the ABIGeneAmp® 7500 Sequence Detection System (Applied Biosystems). In someembodiments, each of these functions can be performed by separatedevices. For example, if one employs a Q-beta replicase reaction foramplification, the reaction may not take place in a thermal cycler, butcould include a light beam emitted at a specific wavelength, detectionof the fluorescent signal, and calculation and display of the amount ofamplification product. In some embodiments, combined thermal cycling andfluorescence detecting devices can be used for precise quantification oftarget nucleic acid sequences in samples. In some embodiments,fluorescent signals can be detected and displayed during and/or afterone or more thermal cycles, thus permitting monitoring of amplificationproducts as the reactions occur in “real time.” In some embodiments, onecan use the amount of amplification product and number of amplificationcycles to calculate how much of the target nucleic acid sequence was inthe sample prior to amplification. In some embodiments, one could simplymonitor the amount of amplification product after a predetermined numberof cycles sufficient to indicate the presence of the target nucleic acidsequence in the sample. One skilled in the art can easily determine, forany given sample type, primer sequence, and reaction condition, how manycycles are sufficient to determine the presence of a given targetpolynucleotide. As used herein, determining the presence of a target cancomprise identifying it, as well as optionally quantifying it. In someembodiments, the amplification products can be scored as positive ornegative as soon as a given number of cycles is complete. In someembodiments, the results may be transmitted electronically directly to adatabase and tabulated. Thus, in some embodiments, large numbers ofsamples can be processed and analyzed with less time and labor when suchan instrument is used. In some embodiments, different detector probesmay distinguish between different target polynucleotides. A non-limitingexample of such a probe is a 5′-nuclease fluorescent probe, such as aTaqMan® probe molecule, wherein a fluorescent molecule is attached to afluorescence-quenching molecule through an oligonucleotide link element.In some embodiments, the oligonucleotide link element of the 5′-nucleasefluorescent probe binds to a specific sequence of an identifying portionor its complement. In some embodiments, different 5′-nucleasefluorescent probes, each fluorescing at different wavelengths, candistinguish between different amplification products within the sameamplification reaction. For example, in some embodiments, one could usetwo different 5′-nuclease fluorescent probes that fluoresce at twodifferent wavelengths (WL_(A) and WL_(B)) and that are specific to twodifferent stem regions of two different extension reaction products (A′and B′, respectively). Amplification product A′ is formed if targetnucleic acid sequence A is in the sample, and amplification product B′is formed if target nucleic acid sequence B is in the sample. In someembodiments, amplification product A′ and/or B′ may form even if theappropriate target nucleic acid sequence is not in the sample, but suchoccurs to a measurably lesser extent than when the appropriate targetnucleic acid sequence is in the sample. After amplification, one candetermine which specific target nucleic acid sequences are present inthe sample based on the wavelength of signal detected and theirintensity. Thus, if an appropriate detectable signal value of onlywavelength WL_(A) is detected, one would know that the sample includestarget nucleic acid sequence A, but not target nucleic acid sequence B.If an appropriate detectable signal value of both wavelengths WL_(A) andWL_(B) are detected, one would know that the sample includes both targetnucleic acid sequence A and target nucleic acid sequence B. In someembodiments, detection can occur through any of a variety of mobilitydependent analytical techniques based on differential rates of migrationbetween different analyte species. Exemplary mobility-dependent analysistechniques include electrophoresis, chromatography, mass spectroscopy,sedimentation, e.g., gradient centrifugation, field-flow fractionation,multi-stage extraction techniques, and the like. In some embodiments,mobility probes can be hybridized to amplification products, and theidentity of the target polynucleotide determined via a mobilitydependent analysis technique of the eluted mobility probes, as describedfor example in Published P.C.T. Application WO04/46344 to Rosenblum etal., and WO01/92579 to Wenz et al. In some embodiments, detection can beachieved by various microarrays and related software such as the AppliedBiosystems Array System with the Applied Biosystems 1700Chemiluminescent Microarray Analyzer and other commercially availablearray systems available from Affymetrix, Agilent, Illumina, and AmershamBiosciences, among others (see also Gerry et al., J. Mol. Biol.292:251-62, 1999; De Bellis et al., Minerva Biotec 14:247-52, 2002; andStears et al., Nat. Med. 9:140-45, including supplements, 2003). It willalso be appreciated that detection can comprise reporter groups that areincorporated into the reaction products, either as part of labeledprimers or due to the incorporation of labeled dNTPs during anamplification, or attached to reaction products, for example but notlimited to, via hybridization tag complements comprising reporter groupsor via linker arms that are integral or attached to reaction products.Detection of unlabeled reaction products, for example using massspectrometry, is also within the scope of the current teachings.

Exemplary Embodiments

FIG. 1 depicts an overview of certain methods according to the presentteachings. Here, a first sample (A) and a second sample (B) are depictedin separate reaction vessels. The first reaction vessel can containtarget polynucleotides (for example micro RNAs) from sample A and thesecond reaction can contain micro RNAs from sample B. For example,sample A can be derived from a wild-type biological source, and sample Bcan be derived from a mutant biological source. Following a treatmentsuch as a reverse transcription reaction to convert the micro RNAs insample A into extension products and the micro RNAs in sample B intoextension products, the two samples can be mixed together into a singlereaction vessel comprising A+B. A collection of decoding reactions canthen be performed to compare the expression levels of micro RNAs betweenthe two samples, using for example real-time PCR on a microfluidic card,or detection by end-point PCR followed by a hybridization array.

FIG. 2A depicts certain compositions according to some embodiments ofthe present teachings. Here, a first linker probe (1) is depicted,illustrating a 3′ target specific portion (3), a stem (4), and a loop(5). Also, a second linker probe (2) is depicted, illustrating a 3′target specific portion (6), a stem (7), and a loop (8). Of note, thestem of the first linker probe (4) is depicted as a solid line, whilethe stem of the second linker probe (7) is depicted as dashed line,indicating that the sequence of the stem of the first linker probe isdifferent from the sequence of the stem of the second linker probe.Accordingly, the stem sequence can considered a zipcode. Thus, theidentity of sample A can be encoded, for example, with a first zipcodesequence located in the stem of the first linker probe, and the identityof sample B can be encoded with a second zipcode sequence located in thestem of the second linker probe. The loop of the first linker probe andthe loop of the second linker probe can comprise the same sequence,which can encode a universal reverse primer

In FIG. 2B (top), a miRNA from a sample A is hybridized to the firstlinker probe (1) in a first reaction vessel, and a miRNA from a sample Bis hybridized to the second linker probe (2) in a second reactionvessel. The species of miRNA from sample A can be considered the same asthe species of miRNA from sample B. Accordingly, the sequence of the 3′target specific portion of the first linker probe (shown as TTCACAC) isthe same as the 3′ target specific portion of the second linker probe(also shown as TTCACAC). Following hybridization of the first linkerprobe to the miRNA in the first reaction vessel and hybridization of thesecond linker probe to the miRNA in the second reaction vessel, one ormore downstream, reactions can be performed. For example, in someembodiments of the present teachings, the linker probes are ligated tothe miRNA molecules in a ligation reaction (middle). The ligationproducts are then subjected to an extension reaction, wherein an enzymesuch as a polymerase and/or reverse transcriptase is employed to extendthe 3′ end of the linker probe to form a strand complementary to thetarget polynucleotide. In some embodiments, the linker probes are notligated to the miRNA molecules, and an extension reaction is performedon the hybridized linker probe/miRNA complex. Following the generationof an extension reaction product in each of the two reaction vessels, asubsequent heating step can degrade the RNA component of the molecule,leaving the newly synthesized strand of nucleic acid in tact (bottom).

As shown in FIG. 2C, the extension products from sample A bearing thefirst linker probe (1), and the extension products from sample B bearingthe second linker probe (2), can be mixed together, and a real-time PCRsuch as TaqMan™ performed. Here, a first detector probe in the PCR isdepicted as solid line with a label (V, indicating the florophore Vic)and a quencher (Q). This first detector probe is designed to query themiRNA extension product from sample A. Further, a second detector probein the PCR is depicted as dashed line with a label (F, indicating theflorophore Earn) and a quencher (Q). This second detector probe isdesigned to query the miRNA extension product from sample B. A miRNAspecific forward primer and a universal reverse primer are included inthe PCR. Thus a single primer pair can be used to amplify the miRNA fromsample A and sample B. The difference in signal between the firstdetector probe and the second detector probe can be used to quantify thedifference in expression level of the miRNA between sample A and sampleB in the real time PCR.

It will be appreciated that in some embodiments of the presentteachings, the loop can correspond to the reverse primer. In someembodiments, the detector probe can correspond with a region of theamplification product corresponding with the 3′ end region of the targetpolynucleotide in the amplification product, as well as a regionupstream from the 3′ end region of the target polynucleotide in theamplification product, as well as the linker probe stem in theamplification product. In some embodiments, the upstream region of thestem, as well as the loop, can correspond to the reverse primer. In someembodiments the detector probe can correspond with the linker probe stemin the amplification product. In some embodiments, the upstream regionof the stem, as well as the loop can correspond to the reverse primer.It will be appreciated that various related strategies for implementingthe different functional regions of these compositions are possible inlight of the present teachings, and that such derivations are routine toone having ordinary skill in the art without undue experimentation.Further illustrative design characteristics of linker probes can befound in FIG. 2 of U.S. Non-Provisional application Ser. No. 10/947,460to Chen et al.

In some embodiments of the present teachings as depicted in FIG. 2, anend point assay can be performed rather than a real-time assay. Forexample, the ratio of Fam/Vic Rn values can determine the relativeabundance of a miRNA in a Sample A as compared to a sample B.

In FIG. 3, an approach for querying miRNAs in two samples is depictedwith a microarray read-out. As shown in FIG. 3A, the stem of the toplinker probe can encode a zipcode 1, whereas the stem of the bottomlinker probe can encode a zipcode N. Thus, a plurality of differentmiRNA species 1-N can be encoded with a plurality of different zipcodes1-N. Further, the sample of origin (A) of a first plurality of miRNAscan be encoded by a universal primer A portion in the tail of eachforward primer, and the sample of origin (B) of a second plurality ofmiRNAs can be encoded by a universal primer B portion in the tail ofeach forward primer. In this situation, an encoding PCR for sample A isperformed in a reaction vessel that is separate from the reaction vesselin which an encoding PCR for sample B is performed. Each encoding PCRcomprises a plurality of target specific forward primers bearing theirappropriate universal tail, as well a reverse primer that was encoded inthe loop of the linker probe. A secondary PCR can then be performed inwhich sample A and sample are mixed together. A universal primer Alabeled with a distinct label (F1-florophore 1) will extend thosetargets derived from sample A, and a universal primer labeled with adifferent distinct label (F2-florophore 2) will extend those targetsderived from sample B. Procedures for ensuring similar Tmcharacteristics and minimal cross-hybridization of primer A and primer Bwill be undertaken to preserve the specificity of the reaction. Theresulting combined labeled. PCR amplicons can then be hybridized to amicroarray for decoding. Here, the microarray comprises spots with thecorresponding complementary zipcode sequences. Thus, a given spot willproduce hybridization for a given species of target polynucleotide. Theratio of signal from F1 to F2 gives a measure of the difference inexpression level for a given target polynucleotide between the twosamples.

The present teachings also contemplate reactions comprisingconfigurations other than a linker probe. For example, in someembodiments, two hybridized molecules with a sticky end can be employed,wherein for example an overlapping 3′ sticky end hybridizes with the 3′end region of the target polynucleotide. Some descriptions of twomolecule configurations that can be employed in the present teachingscan be found in Chen et al., U.S. Non-Provisional application Ser. No.10/982,619. Viewed in light of the present teachings herein, one ofskill in the art will appreciate that the approaches of 10/982,619 canalso be employed to result in extension reaction products that arelonger that the target polynucleotide. These longer products can bedetected with detector probes by, for example, taking advantage of theadditional nucleotides introduced into the reaction products.

Generally however, the loop structure of the present teachings willenhance the Tm of the target polynucleotide-linker probe duplex. Withoutbeing limited to any particular theory, this enhanced Tm could possiblybe due to base stacking effects. Also, the characteristics of the linkerprobe of the present teachings can minimize nonspecific priming duringthe extension reaction, and/or a subsequent amplification reaction suchas PCR. Further, the linker probe of the present teachings can betterdifferentiate mature and precursor forms of miRNA.

The present teachings specifically contemplate embodiments wherein thelinker probe is ligated to the target polynucleotide, as well asembodiments in which the linker probe is hybridized buy not ligated tothe target polynucleotide, as described for example in Chen et al., U.S.Non-Provisional application Ser. No. 10/947,460.

The present teachings also contemplate encoding and decoding reactionschemes, wherein a first encoding extension reaction is followed by asecond decoding amplification reaction, as described for example inAndersen et al., U.S. Non-Provisional application Ser. No. 11/090,830,and Lao et al., U.S. Provisional application Ser. No. 11/090,468.

The present teachings also contemplate a variety of strategies tominimize the number of different molecules in multiplexed amplificationstrategies, as described for example in Whitcombe et al., U.S. Pat. No.6,270,967.

Additional strategies for using the linker probes of the presentteachings in the context of single step assays, as well as in thecontext of small primer compositions, can be found in filed U.S.Non-Provisional application Ser. No. 10/944,153 to Lao and Straus, aswell as in Elfaitouri et al., J. Clin. Virol. 2004, 30(2): 150-156.

Various contexts in which the present teachings can be employed fordiscovery of novel biomarkers for cancer diagnosis and stem celldifferentiation can found in U.S. Provisional Application 60/686,274 toBloch et al.

Kits

In certain embodiments, the present teachings also provide kits designedto expedite performing certain methods. In some embodiments, kits serveto expedite the performance of the methods of interest by assembling twoor more components used in carrying out the methods. In someembodiments, kits may contain components in pre-measured unit amounts tominimize the need for measurements by end-users. In some embodiments,kits may include instructions for performing one or more methods of thepresent teachings. In certain embodiments, the kit components areoptimized to operate in conjunction with one another.

For example, the present teachings provide a kit comprising, a reversetranscriptase, a first linker probe in a first reaction vessel, and asecond linker probe in a second reaction vessel, wherein the firstlinker probe comprises a stem, a loop, and a 3′ target-specific portion,wherein the 3′ target-specific portion corresponds to a miRNA, and thestem encodes a first identifying portion such as a zipcode that encodesthe identity of a first sample of origin, and wherein the second linkerprobe comprises a stem, a loop, and a 3′ target-specific portion,wherein the 3′ target-specific portion corresponds to a miRNA, and thestem encodes a second identifying portion such as a zipcode that encodesthe identity of a second sample of origin. In some embodiments, the kitscan comprise a DNA polymerase. In some embodiments, the kits cancomprise a primer pair. In some embodiments, the kits can furthercomprise a forward primer specific for a miRNA, and, a universal reverseprimer, wherein the universal reverse primer comprises a nucleotide ofthe loop of the linker probe. In some embodiments, the kits can comprisea plurality of primer pairs, wherein each primer pair is in one reactionvessel of a plurality of reaction vessels. In some embodiments, the kitscan comprise a first detector probe and a second detector probe. In someembodiments, the first detector probe comprises a nucleotide of thefirst identifying portion in the first linker probe stem in theamplification product or a nucleotide of the first linker probe stemcomplement in the amplification product, and the first detector probefurther comprises a nucleotide of the 3′ end region of the miRNA in theamplification product or a nucleotide of the 3′ end region of the miRNAcomplement in the amplification product. In some embodiments, the seconddetector probe comprises a nucleotide of the second identifying portionin the second linker probe stem in the amplification product or anucleotide of the second linker probe stem complement in theamplification product, and the second detector probe further comprises anucleotide of the 3′ end region of the miRNA in the amplificationproduct or a nucleotide of the 3′ end region of the miRNA complement inthe amplification product.

The present teachings further contemplate kits comprising a means forhybridizing, a means for ligation, a means for extending, a means foramplifying, a means for detecting, or combinations thereof.

While the present teachings have been described in terms of theseexemplary embodiments, the skilled artisan will readily understand thatnumerous variations and modifications of these exemplary embodiments arepossible without undue experimentation. All such variations andmodifications are within the scope of the current teachings. Aspects ofthe present teachings may be further understood in light of thefollowing examples, which should not be construed as limiting the scopeof the teachings in any way.

Example

A single-plex reaction can be performed on a collection of mouse miRNAsfrom a brain sample and a liver sample to compare the expression levelof a miRNA target polynucleotide.

First, two parallel 6 ul reactions are set up comprising: 1 ul ReverseTranscription Enzyme Mix (Applied Biosystems part number 4340444), 0.5ul dH20, 0.25 ul 2M KCl, 0.05 ul dNTPs (25 mM each), 1 ul 10×RT buffer,0.25 ul Applied Biosystems RNase Inhibitor (10 units/ul), and 2.2 uldH20. Next, 2 ul of the first linker probe (0.25 uM) and RNA samples (2ul of 0.25 ug/ul mouse liver total RNA (Ambion, product number 7810))are added to the first reaction, and, 2 ul of the second linker probe(0.25 uM) and RNA samples (2 ul of 0.25 ug/ul mouse brain total RNA(Ambion, product number 7812)) are added to the second reaction. Next,each reaction is mixed, spun briefly, and placed on ice for 5 minutes.Each reaction is then incubated at 42 C for 30 minutes, followed by 85 Cfor 5° minutes, and then held at 4 C. The reactions are then mixedtogether, and diluted 4 times by adding 30 ul of dH20 prior to the PCRamplification.

A 10 ul PCR amplification is then set up comprising: 2 ul of dilutedreverse transcription reaction product, 1.3 ul 10 uM miRNA specificForward Primer, 0.7 ul 10 uM Universal Reverse Primer, 0.2 ul firstTaqMan detector probe, 0.2 ul second TaqMan detector probe, 0.2 ul dNTPs(25 mM each), 0.6 ul dH20, 5 ul 2× TaqMan master mix (AppliedBiosystems, without UNG). The reaction is started with a 95 C step for10 minutes. Then, 40 cycles are performed, each cycle comprising 95 Cfor 15 seconds, and 60 C for 1 minute. Comparison of the signal from thefirst Taqman detector probe to the second TaqMan detector probe give ameasure of the difference in expression level for the micro RNA ofinterest.

Illustrative designs for various primers and probes applicable to thepresent teachings can be found in U.S. Non-Provisional application Ser.No. 10/947,460, including Table 2.

Although the disclosed teachings have been described with reference tovarious applications, methods, kits, and compositions, it will beappreciated that various changes and modifications may be made withoutdeparting from the teachings herein. The foregoing examples are providedto better illustrate the disclosed teachings and are not intended tolimit the scope of the teachings herein.

1. A kit comprising; a reaction vessel comprising a first linker probe;a reaction vessel comprising a second linker probe; wherein the firstlinker probe and the second linker probe comprise the same 3′ targetspecific portion and different sample identifying portions.
 2. The kitaccording to claim 1 further comprising a reaction vessel comprising areverse transcriptase.
 3. The kit according to claim 1 furthercomprising a reaction vessel comprising a DNA polymerase.
 4. The kitaccording to claim 3 further comprising a primer pair, a first detectorprobe, and a second detector probe, wherein the primer pair, the firstdetector probe, and the second detector probe are present in the samereaction vessel.
 5. The kit according to claim 4 wherein the primer paircomprises, a forward primer specific for a small target polynucleotide,and, a universal reverse primer, wherein the universal reverse primer isencoded in the loop of the first linker probe and the second linkerprobe.
 6. A reaction mixture comprising; a first linker probe hybridizedto a first species of a small target polynucleotide, and a second linkerprobe hybridized to a second species of the small target polynucleotide,wherein the first linker probe comprises a first sample identifyingportion and the second linker probe comprises a second sampleidentifying portion.
 7. The reaction mixture according to claim 6further comprising a reverse transcriptase.
 8. The reaction mixtureaccording to claim 6 further comprising a forward primer specific forthe small target polynucleotide, and a reverse primer, wherein thereverse primer is encoded in a loop of the first linker probe and a loopof the second linker probe, and wherein the sequence of the loop of thefirst linker probe encoding the reverse primer is the same as thesequence of the loop of the second linker probe encoding the reverseprimer.